Weighted Single-Step Genome-Wide Association Study for Growth Traits in Chinese Simmental Beef Cattle

Improving the genetic process of growth traits is one of the major goals in the beef cattle industry, as it can increase meat production and reduce the cost of raising animals. Although several quantitative trait loci affecting growth traits in beef cattle have been identified, the genetic architecture of these economically important traits remains elusive. This study aims to map single nucleotide polymorphisms (SNPs) and genes associated with birth weight (BW), yearling weight (YW), average daily gain from birth to yearling (BYADG), and body weight at the age of 18 months (18MW) in a Chinese Simmental beef cattle population using a weighted, single-step, genome-wide association study (wssGWAS). Phenotypic and pedigree data from 6022 animals and genotypes from 744 animals (596,297 SNPs) were used for an association analysis. The results showed that 66 genomic windows explained 1.01–20.15% of the genetic variance for the four examined traits, together with the genes near the top SNP within each window. Furthermore, the identified genomic windows (>1%) explained 50.56%, 57.71%, 61.78%, and 37.82% of the genetic variances for BW, YW, BYADG, and 18MW, respectively. Genes with potential functions in muscle development and regulation of cell growth were highlighted as candidates for growth traits in Simmental cattle (SQOR and TBCB for BW, MYH10 for YW, RLF for BYADG, and ARHGAP31 for 18MW). Moreover, we found 40 SNPs that had not previously been identified as being associated with growth traits in cattle. These findings will further advance our understanding of the genetic basis for growth traits and will be useful for the molecular breeding of BW, YW, BYADG, and 18MW in the context of genomic selection in beef cattle.

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Integration of a single-step genome-wide association study with a multi-tissue transcriptome analysis provides novel insights into the genetic basis of wool and weight traits in sheep

Genetics Selection Evolution ◽

10.1186/s12711-021-00649-8 ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Bingru Zhao ◽

Hanpeng Luo ◽

Xixia Huang ◽

Chen Wei ◽

Jiang Di ◽

...

Keyword(s):

Association Study ◽

Candidate Genes ◽

Genetic Improvement ◽

Genome Wide Association Study ◽

Growth Traits ◽

Fibre Diameter ◽

Single Step ◽

Genome Wide Association ◽

Six Traits ◽

Genome Wide

Abstract Background Genetic improvement of wool and growth traits is a major goal in the sheep industry, but their underlying genetic architecture remains elusive. To improve our understanding of these mechanisms, we conducted a weighted single-step genome-wide association study (WssGWAS) and then integrated the results with large-scale transcriptome data for five wool traits and one growth trait in Merino sheep: mean fibre diameter (MFD), coefficient of variation of the fibre diameter (CVFD), crimp number (CN), mean staple length (MSL), greasy fleece weight (GFW), and live weight (LW). Results Our dataset comprised 7135 individuals with phenotype data, among which 1217 had high-density (HD) genotype data (n = 372,534). The genotypes of 707 of these animals were imputed from the Illumina Ovine single nucleotide polymorphism (SNP) 54 BeadChip to the HD Array. The heritability of these traits ranged from 0.05 (CVFD) to 0.36 (MFD), and between-trait genetic correlations ranged from − 0.44 (CN vs. LW) to 0.77 (GFW vs. LW). By integrating the GWAS signals with RNA-seq data from 500 samples (representing 87 tissue types from 16 animals), we detected tissues that were relevant to each of the six traits, e.g. liver, muscle and the gastrointestinal (GI) tract were the most relevant tissues for LW, and leukocytes and macrophages were the most relevant cells for CN. For the six traits, 54 quantitative trait loci (QTL) were identified covering 81 candidate genes on 21 ovine autosomes. Multiple candidate genes showed strong tissue-specific expression, e.g. BNC1 (associated with MFD) and CHRNB1 (LW) were specifically expressed in skin and muscle, respectively. By conducting phenome-wide association studies (PheWAS) in humans, we found that orthologues of several of these candidate genes were significantly (FDR < 0.05) associated with similar traits in humans, e.g. BNC1 was significantly associated with MFD in sheep and with hair colour in humans, and CHRNB1 was significantly associated with LW in sheep and with body mass index in humans. Conclusions Our findings provide novel insights into the biological and genetic mechanisms underlying wool and growth traits, and thus will contribute to the genetic improvement and gene mapping of complex traits in sheep.

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PSXI-7 Genomic analysis of heterosis in a composite beef cattle breed

Journal of Animal Science ◽

10.1093/jas/skab235.445 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 244-244

Author(s):

El Hamidi Hay ◽

Andrew Roberts

Keyword(s):

Birth Weight ◽

Beef Cattle ◽

Association Study ◽

Genome Wide Association Study ◽

Growth Traits ◽

Snp Markers ◽

Genome Wide Association ◽

Weaning Weight ◽

Genome Wide ◽

A Genome

Abstract Crossbreeding is widely used in the beef cattle industry to exploit benefits of heterosis. This study evaluated the effects of heterozygosity on growth traits in an Angus x Hereford cross population. Moreover, a genome wide association study was conducted to detect regions in the genome with significant dominance effects on growth traits contributing to heterosis. A total of 1,530 animals, comprised of pure Line 1 Hereford, Angus and Angus x Line 1 Hereford crosses, were evaluated. Phenotypes included birth weight, weaning weight and yearling weight. All animals were genotyped with GeneSeek GGP LD 50k. Effects of genomic heterozygosity on growth traits were estimated. These effects were -0.76 kg (P < 0.001), 4.67 kg (P < 0.0001), 42.39 kg (P < 0.02) on birth weight, weaning weight and yearling weight respectively. A genome wide association study revealed several SNP markers with significant heterotic effects associated with birth weight, weaning weight and yearling weight. These SNP markers were located on chromosomes 1, 2, 14, 19, 13 and 12. Genes in these regions were reported to be involved in growth and other important physiological mechanisms. Our study revealed several regions associated with dominance effects and contributing to heterosis. These results could be beneficial in optimizing crossbreeding.

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Genome-wide association study for feed efficiency and growth traits in U.S. beef cattle

BMC Genomics ◽

10.1186/s12864-017-3754-y ◽

2017 ◽

Vol 18 (1) ◽

Cited By ~ 54

Author(s):

Christopher M. Seabury ◽

David L. Oldeschulte ◽

Mahdi Saatchi ◽

Jonathan E. Beever ◽

Jared E. Decker ◽

...

Keyword(s):

Beef Cattle ◽

Association Study ◽

Feed Efficiency ◽

Genome Wide Association Study ◽

Growth Traits ◽

Genome Wide Association ◽

Genome Wide

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27. Genome wide association study for compensatory growth in Irish beef cattle

Animal - science proceedings ◽

10.1016/j.anscip.2021.03.028 ◽

2021 ◽

Vol 12 (1) ◽

pp. 17

Author(s):

Yvonne Mullins ◽

Alan Kelly ◽

David Kenny ◽

Sinead Waters

Keyword(s):

Beef Cattle ◽

Association Study ◽

Compensatory Growth ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide

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Genome-wide association study of growth and body composition traits in Brangus beef cattle

Livestock Science ◽

10.1016/j.livsci.2015.11.011 ◽

2016 ◽

Vol 183 ◽

pp. 4-11 ◽

Cited By ~ 14

Author(s):

Ziqing Weng ◽

Hailin Su ◽

Mahdi Saatchi ◽

Jungjae Lee ◽

Milton G. Thomas ◽

...

Keyword(s):

Body Composition ◽

Beef Cattle ◽

Association Study ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide

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Genome-wide association for heifer reproduction and calf performance traits in beef cattle

Genome ◽

10.1139/gen-2015-0031 ◽

2015 ◽

Vol 58 (12) ◽

pp. 549-557 ◽

Cited By ~ 5

Author(s):

Everestus C. Akanno ◽

Graham Plastow ◽

Carolyn Fitzsimmons ◽

Stephen P. Miller ◽

Vern Baron ◽

...

Keyword(s):

Beef Cattle ◽

Genome Wide Association Study ◽

Average Daily Gain ◽

Snp Markers ◽

Genome Wide Association ◽

Research Centre ◽

Genome Wide ◽

A Genome ◽

Starting Point ◽

And Performance

The aim of this study was to identify SNP markers that associate with variation in beef heifer reproduction and performance of their calves. A genome-wide association study was performed by means of the generalized quasi-likelihood score (GQLS) method using heifer genotypes from the BovineSNP50 BeadChip and estimated breeding values for pre-breeding body weight (PBW), pregnancy rate (PR), calving difficulty (CD), age at first calving (AFC), calf birth weight (BWT), calf weaning weight (WWT), and calf pre-weaning average daily gain (ADG). Data consisted of 785 replacement heifers from three Canadian research herds, namely Brandon Research Centre, Brandon, Manitoba, University of Alberta Roy Berg Kinsella Ranch, Kinsella, Alberta, and Lacombe Research Centre, Lacombe, Alberta. After applying a false discovery rate correction at a 5% significance level, a total of 4, 3, 3, 9, 6, 2, and 1 SNPs were significantly associated with PBW, PR, CD, AFC, BWT, WWT, and ADG, respectively. These SNPs were located on chromosomes 1, 5–7, 9, 13–16, 19–21, 24, 25, and 27–29. Chromosomes 1, 5, and 24 had SNPs with pleiotropic effects. New significant SNPs that impact functional traits were detected, many of which have not been previously reported. The results of this study support quantitative genetic studies related to the inheritance of these traits, and provides new knowledge regarding beef cattle quantitative trait loci effects. The identification of these SNPs provides a starting point to identify genes affecting heifer reproduction traits and performance of their calves (BWT, WWT, and ADG). They also contribute to a better understanding of the biology underlying these traits and will be potentially useful in marker- and genome-assisted selection and management.

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